5kqj - Revision history

OCA at 10:13, 14 June 2023

OCA — Wed, 14 Jun 2023 10:13:39 GMT

←Older revision		Revision as of 10:13, 14 June 2023
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	==Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics==		==Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics==
-	<StructureSection load='5kqj' size='340' side='right'caption='[[5kqj~~]], [[NMR_Ensembles_of_Models \| 15 NMR models~~]]' scene=''>	+	<StructureSection load='5kqj' size='340' side='right'caption='[[5kqj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus~~ pneumoniae~~" (schroeter 1886) flugge 1886~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aadB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqj OCA], [https://pdbe.org/5kqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kqj RCSB], [https://www.ebi.ac.uk/pdbsum/5kqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqj ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.46 2.7.7.46] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqj OCA], [~~http~~://pdbe.org/5kqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AADB1_KLEPN AADB1_KLEPN]] This enzyme confers resistance to kanamycin, gentamicin, dibekacin, sisomicin and tobramycin by adenylating the 2''-hydroxyl group of these antibiotics.	+	[https://www.uniprot.org/uniprot/AADB1_KLEPN AADB1_KLEPN] This enzyme confers resistance to kanamycin, gentamicin, dibekacin, sisomicin and tobramycin by adenylating the 2''-hydroxyl group of these antibiotics.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Klebsiella pneumoniae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Transferase]]~~	+	[[Category: Bacot-Davis VR]]
-	[[Category: Bacot-Davis~~, V R~~]]	+	[[Category: Berghuis AM]]
-	[[Category: Berghuis~~, A M]]~~	+
-	~~[[Category: Aminoglycoside]]~~	+
-	~~[[Category: Antibiotic resistance~~]]	+

OCA at 08:10, 8 January 2020

OCA — Wed, 08 Jan 2020 08:10:38 GMT

←Older revision		Revision as of 08:10, 8 January 2020
Line 1:		Line 1:

	==Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics==		==Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics==
-	<StructureSection load='5kqj' size='340' side='right' caption='[[5kqj]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>	+	<StructureSection load='5kqj' size='340' side='right'caption='[[5kqj]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Bacot-Davis, V R]]		[[Category: Bacot-Davis, V R]]

OCA at 10:09, 15 November 2017

OCA — Wed, 15 Nov 2017 10:09:42 GMT

←Older revision		Revision as of 10:09, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5kqj' size='340' side='right' caption='[[5kqj]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='5kqj' size='340' side='right' caption='[[5kqj]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pneumoniae"_(schroeter_1886)_flugge_1886 "bacillus pneumoniae" (schroeter 1886) flugge 1886]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.46 2.7.7.46] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aadB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=573 "Bacillus pneumoniae" (Schroeter 1886) Flugge 1886])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.46 2.7.7.46] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqj OCA], [http://pdbe.org/5kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqj RCSB], [http://www.ebi.ac.uk/pdbsum/5kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqj OCA], [http://pdbe.org/5kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqj RCSB], [http://www.ebi.ac.uk/pdbsum/5kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AADB1_KLEPN AADB1_KLEPN]] This enzyme confers resistance to kanamycin, gentamicin, dibekacin, sisomicin and tobramycin by adenylating the 2''-hydroxyl group of these antibiotics.		[[http://www.uniprot.org/uniprot/AADB1_KLEPN AADB1_KLEPN]] This enzyme confers resistance to kanamycin, gentamicin, dibekacin, sisomicin and tobramycin by adenylating the 2''-hydroxyl group of these antibiotics.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The aminoglycoside modifying enzyme (AME) ANT(2'')-Ia is a significant target for next generation antibiotic development. Structural studies of a related aminoglycoside-modifying enzyme, ANT(3'')(9), revealed this enzyme contains dynamic, disordered, and well-defined segments that modulate thermodynamically before and after antibiotic binding. Characterizing these structural dynamics is critical for in situ screening, design, and development of contemporary antibiotics that can be implemented in a clinical setting to treat potentially lethal, antibiotic resistant, human infections. Here, the first NMR structural ensembles of ANT(2'')-Ia are presented, and suggest that ATP-aminoglycoside binding repositions the nucleotidyltransferase (NT) and C-terminal domains for catalysis to efficiently occur. Residues involved in ligand recognition were assessed by site-directed mutagenesis. In vitro activity assays indicate a critical role for I129 toward aminoglycoside modification in addition to known catalytic D44, D46, and D48 residues. These observations support previous claims that ANT aminoglycoside sub-class promiscuity is not solely due to binding cleft size, or inherent partial disorder, but can be controlled by ligand modulation on distinct dynamic and thermodynamic properties of ANTs under cellular conditions. Hydrophobic interactions in the substrate binding cleft, as well as solution dynamics in the C-terminal tail of ANT(2'')-Ia, advocate toward design of kanamycin-derived cationic lipid aminoglycoside analogs, some of which have already shown antimicrobial activity in vivo against kanamycin and gentamicin-resistant P. aeruginosa. This data will drive additional in silico, next generation antibiotic development for future human use to combat increasingly prevalent antimicrobial resistance.
		+
		+	Effect of solvent and protein dynamics in ligand recognition and inhibition of aminoglycoside adenyltransferase 2''-Ia.,Bacot-Davis VR, Bassenden AV, Sprules T, Berghuis AM Protein Sci. 2017 Sep;26(9):1852-1863. doi: 10.1002/pro.3224. Epub 2017 Jul 21. PMID:28734024<ref>PMID:28734024</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kqj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:13, 10 September 2017

OCA — Sun, 10 Sep 2017 10:13:01 GMT

←Older revision		Revision as of 10:13, 10 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5kqj is ON HOLD until Paper Publication~~	+	==Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics==
-		+	<StructureSection load='5kqj' size='340' side='right' caption='[[5kqj]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
-	~~Authors: Bacot-Davis, V.R., Berghuis, A.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kqj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KQJ FirstGlance]. <br>
-	~~Description:~~ Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.46 2.7.7.46] </span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5kqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kqj OCA], [http://pdbe.org/5kqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kqj RCSB], [http://www.ebi.ac.uk/pdbsum/5kqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kqj ProSAT]</span></td></tr>
-	[[Category: Bacot-Davis, V.R]]	+	</table>
-	[[Category: Berghuis, A.M]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AADB1_KLEPN AADB1_KLEPN]] This enzyme confers resistance to kanamycin, gentamicin, dibekacin, sisomicin and tobramycin by adenylating the 2''-hydroxyl group of these antibiotics.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Transferase]]
		+	[[Category: Bacot-Davis, V R]]
		+	[[Category: Berghuis, A M]]
		+	[[Category: Aminoglycoside]]
		+	[[Category: Antibiotic resistance]]

OCA at 10:22, 9 March 2017

OCA — Thu, 09 Mar 2017 10:22:33 GMT

←Older revision		Revision as of 10:22, 9 March 2017
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	Description: Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics		Description: Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Berghuis, A.M]]
	[[Category: Bacot-Davis, V.R]]		[[Category: Bacot-Davis, V.R]]
		+	[[Category: Berghuis, A.M]]

OCA at 12:43, 26 July 2016

OCA — Tue, 26 Jul 2016 12:43:25 GMT

←Older revision		Revision as of 12:43, 26 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kqj is ON HOLD	+	The entry 5kqj is ON HOLD until Paper Publication

	Authors: Bacot-Davis, V.R., Berghuis, A.M.		Authors: Bacot-Davis, V.R., Berghuis, A.M.

OCA: Protected "5kqj" [edit=sysop:move=sysop]

OCA — Thu, 14 Jul 2016 09:35:20 GMT

Protected "5kqj" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:35, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kqj is ON HOLD Authors: Bacot-Davis, V.R., Berghuis, A.M. Description: Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Subs...

OCA — Thu, 14 Jul 2016 09:35:18 GMT

New page: '''Unreleased structure''' The entry 5kqj is ON HOLD Authors: Bacot-Davis, V.R., Berghuis, A.M. Description: Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Subs...

New page

'''Unreleased structure'''

The entry 5kqj is ON HOLD

Authors: Bacot-Davis, V.R., Berghuis, A.M.

Description: Solution Structure of Antibiotic-Resistance Factor ANT(2'')-Ia Reveals Substrate-Regulated Conformation Dynamics
[[Category: Unreleased Structures]]
[[Category: Berghuis, A.M]]
[[Category: Bacot-Davis, V.R]]